And then there are the pumps. Naturally brackish, the delta is now managed as a freshwater system, because fresh water is what's needed to fill bathtubs and irrigate fields and quench the thirst of Californians, about 25 million of whom rely on the delta for at least some of their water. Mammoth federal and state pumps in the delta's southern end, near the city of Tracy, slurp up roughly half of the Sacramento's flow and send it to Silicon Valley, Los Angeles and beyond. When the federal pumps are going full blast, six 22,500-horsepower motors pull water through pipes 15 feet in diameter, raising the flow into a canal that helps irrigate the middle of California's Central Valley. (The state pumps are even bigger.)

The pumps are powerful enough to alter the currents miles away, confusing migrating salmon. Often, salmon are siphoned along with the water. More than half of these are salvaged near the pumps at fish-collection facilities, where the buckets are checked every two hours, the operators pawing through seaweed to find the tiny fish, which are then loaded into trucks and driven back to the delta. But the smallest chinooks can slip through; in past years tens of thousands have died. In 2005, that fateful year for this season's salmon, the pumps exported record amounts of water from the delta.

"The higher the export rate, the more fish are lost," said Tina Swanson, a biologist and head of the Bay Institute, an advocacy group that monitors San Francisco Bay and the delta. "Even small increases can lead to disproportionately high losses."

Constructed mostly in the middle of the last century, the pumps are relics of a time when fish populations were not much valued or understood. Lately California's attitude has changed. When I visited the federal pumps, they were churning much more slowly than usual because of a court order to protect a threatened fish called the delta smelt. Already, farmers to the south were not getting water they'd asked for. They were also nervous about another lawsuit, filed by a coalition of environmentalists, fishing associations and Native Americans on behalf of the Sacramento's winter-run chinook and other salmon species. Among other things, the plaintiffs want more reliable cold releases from the Shasta reservoir, which could limit flows to the pumps.

"I can't be without [that] water," said Daniel Errotabere, co-owner of Errotabere Ranch, which grows some 5,600 acres of almonds, lettuce and other crops with the help of delta flows. This summer the farm got just 40 percent of the water it had ordered from the pumps. "We're not wasting anything. All our crops are pretty much spoonfed. I can't do any more than I'm doing, unless there's a way to find a crop that doesn't need water."

My guide to the fantastical Sacramento-San Joaquin Delta was Peter Moyle, of the University of California at Davis, an estuary and fish expert who made room on his research boat to show me a bit of what the delta is and used to be. I wanted to see some wild baby salmon, which he said was not likely, since it was late in a dry spring. I felt sure he would be relieved to see some too. When I picked him up in Davis, there were salmon prayer flags fluttering in front of his house.

Moyle has spent much of the past 30 years in the grayish-brown marsh mud on the outskirts of the delta, and he's the authority on local fish—the California roach, the Sacramento sucker, the tule perch—much less glamorous than salmon. He's the go-to person on the delta smelt, a homely little fish that smells like cucumber and faces many of the same challenges as the chinook.

Moyle's rickety aluminum research vessel, The Marsh Boat, was crewed by two graduate students. We pulled on waders and life vests and then bounced off into a stiff north wind, which made the tall grasses on the shore roll like waves. We were surveying fish populations on the outskirts of the delta in the Suisun Marsh, which has not been tampered with as much as adjoining areas and is reminiscent of what the whole place might have looked like before the gold rush: an expanse of bulrushes and brownish water, with snowy egrets stalking the perimeter and white pelicans flapping overhead. It was almost possible to ignore the bellow of an Amtrak train bound for San Francisco and the jets landing at nearby Travis Air Force Base.

The boat stopped by a muddy beach, depositing Moyle, me and a graduate student studying invasive jellyfish from the Caspian Sea. The other student roared off in hot pursuit of zooplankton. We walked the shore, with the professor periodically plunging into the water to drag a net. "If you were a baby salmon, this is exactly where you'd want to be," said Moyle, his bifocal sunglasses glinting as he eyed a particularly inviting stand of bulrushes. "This would have been full of food, full of cover. You could have escaped your predators and there were strong enough currents that you could find your way out to sea."

Nearly everyone's unhappy with the delta as it is today. Some say that rising sea levels and earthquakes threaten its structure, and since Hurricane Katrina there have been calls to armor the levees to maintain the delta as a freshwater system. Others advocate reducing water exports from the delta, doing away with the levees and unleashing the river to become brackish again in places and flow where it will.

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